This section contains a summary of Babylon 5's story arc (the 5-year plotline) up to, but not including, "There All the Honor Lies." Note that this is chock full of spoilers!
Season One began with an attack, then backed off to allow time to introduce most of the major characters, species, and forces and touch on most of the themes, only to gather force again at the end with a set of intense episodes that raise as many questions as they resolve. The prominent threads are the Centauri-Narn conflict, the Shadows, the Psi Corps, happenings on Earth, the Minbari surrender, what happened to Sinclair at the Battle of the Line, what happened to the previous Babylon stations, and the Vorlons.
As the season began, the Narns launched a preemptive and unprovoked strike against a Centauri agricultural outpost ("Midnight on the Firing Line.") The official Centauri response was to do nothing, but due to his personal involvement with events there and his great desire that the Centauri show the mettle of their former age of empire, the somewhat foppish Ambassador Londo Mollari, with the sympathetic support of the humans and Minbari, tried to defy his government and sanction the Narn. The two sides continued to bicker until in exasperation Londo called for help from his new friend Mr. Morden. The Shadows launched a preemptive and unprovoked strike against a Narn outpost ("Chrysalis") -- and utterly destroyed it (to Londo's moderate distress.)
The first encounter B5 had with the Shadows occured when a mysterious, polite man named Morden arrived and asked each of the alien ambassadors, "What do you want?" ("Signs and Portents") Delenn suspected what Morden represented; Kosh certainly knew; G'Kar only wanted to annihilate the Centauri. Morden seemed to approve most of Londo's desire for the Centauri to reclaim their lost empire, so he ingratiated himself by doing Londo a great favor. It was only after the Shadows attacked the Narn that G'Kar made a connection between this new enemy and an ancient enemy of lore. He traveled to the rim of known space and found a deadly force on Z'ha'dum, a world thought to be long dead ("Revelations.") However, his unconfirmed warnings of a great threat fell, and continue to fall, on deaf ears in the council chambers.
Almost as secretive, and certainly as nefarious, is the Psi Corps. Although Talia is reasonable and ethical, the behavior of her superiors in the organization is questionable. Among many who view the Corps with suspicion, Ivanova's hatred of them is almost legendary. They hunted Jason Ironheart to the station because after completing their experiments on him he could see into their machinations for global domination ("Mind War.") The Corps' security arm, the Psi Cops, as represented by Bester, appear to be a particularly sinister breed.
The idea that the Psi Corps might be manipulating the Earth government was lent confirmation when a connection arose between them and the assassination of the Earth President and the installment of his successor ("Revelations.") There are other ominous signs of changes coming from Earth, among them the anti-alien Homeguard ("The War Prayer") and the squelching of the Mars independence movement ("A Voice in the Wilderness.") Whatever the cause, things "back home" are becoming continuously bleaker.
Twelve years ago humans were responsible for the death of the Minbari leader. In retaliation, the Minbari declared war, and in the final hour, as their ships were poised for the destruction of Earth, the Minbari Grey Council captured one human, Sinclair, attempting to ram their ship. In the course of their interrogation they discovered to their horror that Minbari souls were being reborn in human bodies. Because Minbari refuse to harm their own, and due to an ancient prophecy regarding the joining of their souls and the fight against a great enemy, the Grey Council ordered the Minbari to surrender. They maintained an interest in Sinclair, however, and effectively selected him to run B5. They also invited him to Minbar as the first Earth ambassador ("Points of Departure.")
Delenn, who was present at the questioning of Sinclair, was chosen by the Grey Council to be the leader of the Minbari ("Babylon Squared.") So deep was her belief in the prophecy and her role to play in fulfilling it that she not only declined the nomination but defied the Council's orders, spinning a cocoon and metamorphosing into a Minbari-Human hybrid. Perhaps she is right, for the instant a "Soul Hunter" (a caretaker of the "greatest souls") saw her, he tried to collect her soul prematurely.
The first three Babylon stations were sabotaged. The fourth vanished immediately after coming online. Four years later it reappeared and a strange alien named Zathras explained that B4 was being drawn through time by "The One," (a much older Sinclair aided by Delenn) to serve in a great galactic war ("Babylon Squared.") People on B4 experienced time shifts, and Sinclair envisioned Garibaldi's last stand in a battle aboard B5.
The Vorlons are almost as much a mystery at the end of the season as at the beginning. As Kosh arrived on the station ("The Gathering") he was the victim of an assassination attempt by a Minbari. Lest we think the Vorlons are ineffectual or completely uninvolved, they enigmatically destroyed a ship bearing the secret of immortality to Earth. Kosh also showed an interest in Talia, to the point of making a mental recording of her ("Deathwalker.")
The planet below B5 was found to contain vastly powerful machinery and weapons. Delenn's former mentor Draal replaced the sentient heart of the machine ("A Voice in the Wilderness.")
In "The Geometry of Shadows," Refa, a high-ranking Centauri noble, asked Londo to pledge his help in seizing the throne at some point.
In "A Distant Star," Lt. Keffer saw a Shadow ship in hyperspace and vowed to find out what it was.
"A Spider in the Web" revealed a mysterious "Bureau 13" operating out of the San Diego wastelands. An assassin, controlled by the Bureau, attempted to thwart a peaceful settlement of the situation on Mars. Scanning his mind, Talia saw a Psi Cop present at the operation that programmed the assassin, but she didn't tell anybody else. Sheridan's interest in conspiracy theories was revealed as he attempted to solve the puzzle, and the existence of a plant among the B5 crew, code-named Control, was hinted at.
In "Soul Mates," Londo's three wives came to the station; one, who knows G'Kar, tried to murder him. He divorced her and one of the others. Talia's ex-husband, from an arranged marriage courtesy of the Corps, tried to woo her back.
In "A Race Through Dark Places," Bester returned to Babylon 5. He believed an underground railroad was smuggling unregistered telepaths outside of Psi-Corps' control. Talia was captured by the rogue telepaths and told gruesome stories of the Corps' true nature: forced breeding, murder, and coercion. She and the others tricked Bester into thinking the railroad was stopped. Dr. Franklin was revealed as one of the railroad's participants. Talia discovered another part of Ironheart's "gift" -- she is apparently now immune to telepathic scans.
At Refa's behest, as the Centauri emperor lay dying, Londo asked Morden to destroy a major Narn colony in "The Coming of Shadows." The Narns, believing the Centauri military responsible, declared war. Sinclair sent a message to Garibaldi via a network of "rangers," spies, a group he apparently heads.
In "All Alone in the Night," Delenn was removed from the Grey Council, and a member of the warrior caste replaced her. We learned that Sheridan had been secretly evaluating the loyalty of the station's command staff, and is in league with a group (headed by General Hague, a member of the Joint Chiefs of Staff) out to expose what they believe is an attempt by the Psi-Corps and others to control the government. Of special note is a densely-packed dream sequence in which Sheridan is visited by Ambassador Kosh.
President Clark's personal physician fled to the station in "Hunter, Prey" with files proving that Clark wasn't sick as he claimed when he left Earth Force One just before it blew up and killed President Santiago. Sheridan gave the files to a representative of General Hague. Kosh agreed to teach Sheridan until he is ready "to fight legends" -- at which point it was implied Kosh would reveal himself to Sheridan.